Fix workflow graphs.

Author: tsalo

xcp_d/data/tests/config.toml

@@ -26,17 +26,15 @@ run_uuid = "20240205-123456"
 templateflow_home = "~/.cache/templateflow"
 work_dir = "work/"
 write_graph = false
+atlases = ["Gordon"]
 
 [workflow]
-cifti = false
+file_format = "nifti"
 dummy_scans = 0
 input_type = "fmriprep"
 despike = false
 smoothing = 6
 combine_runs = false
-motion_filter_type = false
-band_stop_min = false
-band_stop_max = false
 motion_filter_order = 4
 head_radius = 50
 fd_thresh = 0.3
@@ -45,7 +43,6 @@ bandpass_filter = true
 high_pass = 0.01
 low_pass = 0.1
 bpf_order = 2
-atlases = []
 min_coverage = 0.5
 correlation_lengths = []
 process_surfaces = false

xcp_d/workflows/bold/cifti.py

@@ -63,9 +63,9 @@ def init_postprocess_cifti_wf(
 
                 run_data = collect_run_data(
                     layout=layout,
-                    input_type="fmriprep",
                     bold_file=bold_file,
-                    cifti=True,
+                    file_format="cifti",
+                    target_space="fsLR",
                 )
 
                 from xcp_d.utils.utils import _create_mem_gb

xcp_d/workflows/bold/metrics.py

@@ -274,7 +274,7 @@ def init_reho_cifti_wf(
             with mock_config():
                 wf = init_reho_cifti_wf(
                     name_source="/path/to/bold.dtseries.nii",
-                    mem_gb={"volume": 0.1},
+                    mem_gb={"bold": 0.1},
                     name="cifti_reho_wf",
                 )
 
@@ -442,7 +442,7 @@ def init_reho_nifti_wf(name_source, mem_gb, name='reho_nifti_wf'):
             with mock_config():
                 wf = init_reho_nifti_wf(
                     name_source="/path/to/bold.nii.gz",
-                    mem_gb={"volume": 0.1},
+                    mem_gb={"bold": 0.1},
                     name="nifti_reho_wf",
                 )
 

xcp_d/workflows/bold/nifti.py

@@ -66,9 +66,9 @@ def init_postprocess_nifti_wf(
 
                 run_data = collect_run_data(
                     layout=layout,
-                    input_type="fmriprep",
                     bold_file=bold_file,
-                    cifti=False,
+                    file_format="nifti",
+                    target_space="MNI152NLin2009cAsym",
                 )
 
                 from xcp_d.utils.utils import _create_mem_gb

xcp_d/workflows/bold/plotting.py

@@ -484,7 +484,13 @@ def init_execsummary_functional_plots_wf(
 
             with mock_config():
                 wf = init_execsummary_functional_plots_wf(
-                    preproc_nifti=None,
+                    preproc_nifti=str(
+                        config.execution.fmri_dir / "sub-01" / "func" /
+                        (
+                            "sub-01_task-imagery_run-01_space-MNI152NLin2009cAsym_res-2_"
+                            "desc-preproc_bold.nii.gz"
+                        )
+                    ),
                     t1w_available=True,
                     t2w_available=True,
                     mem_gb={"bold": 1},

xcp_d/workflows/parcellation.py

@@ -28,9 +28,13 @@ def init_load_atlases_wf(name='load_atlases_wf'):
 
             from xcp_d.tests.tests import mock_config
             from xcp_d import config
+            from xcp_d.data import load as load_data
             from xcp_d.workflows.parcellation import init_load_atlases_wf
 
             with mock_config():
+                config.execution.datasets = {
+                    "xcpdatlases": str(load_data("atlases")),
+                }
                 wf = init_load_atlases_wf()
 
     Parameters